Although this AU mostly follows canon, there are some differences specifically in the endgame.
* Vanitas is much, much stronger than in canon. This is especially important because when he merges with Ven, he reigns supreme and gains full control of his body. Aqua gets defeated, but not killed, as Terra manages to leave Master Xehanort briefly in order to save Aqua and Ven. However, it's already too late, and Terra is left with the task of 'erasing' Ventus, as he requested.
* Master Xehanort faces Terra immediately after, going straight to him. However, unlike in canon, when Master Xehanort sends his heart into Terra, Terra's darkness and the strength of his heart are so strong that Master Xehanort's heart is completely absorbed, giving Terra access to all of Xehanort's talents and intellect, all while warping his appearance.
* The big explosion from Kingdom Hearts then occurs as it did in canon. Terranort is sent to Radiant Garden with Aqua's scattered armor and Keyblade, which were separated from her in the fight against Vanitas/Ven. Aqua herself goes straight to the Mysterious Tower with Ven's sleeping body. Canon essentially resumes...at least, until Aqua creates the Chamber of Waking.
* Somehow, Vanitas managed to survive in a new form...the Vanitas Sentiment. He arrives, aiming to finish the job with Aqua, but instead she winds up falling into the realm of darkness, where she remains for many years.
* Vanitas Sentiment still exists even in the present timeline, mostly just lurking behind the scenes.